Variations in DNA methylation patterns during the cell cycle of HeLa cells

Epigenetics

Volumn 2, Issue 1, 2007, Pages 54-65

  Brown, Shelley E ^a   Fraga, Mario F ^b   Weaver, Ian C G ^a   Berdasco, Maria ^b   Szyf, Moshe ^a  

^a MCGILL UNIVERSITY   (Canada)

^b Centro Nacional de Investigaciones Oncológicas   (Spain)

Author keywords

Cancer; Cell cycle; CpG microarray; DNA methylation; Epigenetics; Repetitive sequences

Indexed keywords

CYTOSINE; DNA; GUANINE;

ARTICLE; CELL CYCLE; CELL CYCLE G0 PHASE; CELL CYCLE G1 PHASE; CELL CYCLE S PHASE; CELL DIVISION; CELL MATURATION; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; DNA MICROARRAY; DNA SEQUENCE; HELA CELL; HUMAN; HUMAN CELL; IMMUNOCYTOCHEMISTRY; NUCLEOTIDE SEQUENCE; SOMATIC CELL;

EID: 34249672387     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.4161/epi.2.1.3880     Document Type: Article

References (71)

1. Razin A. CpG methylation, chromatin structure and gene silencing-a three-way connection. EMBO J 1998; 17:4905-8.
2. Razin A, Riggs AD. DNA methylation and gene function. Science 1980; 210:604-10.
3. Gruenbaum Y, Stein R, Cedar H, Razin A. Methylation of CpG sequences in eukaryotic DNA. FEBS Lett 1981; 124:67-71.
4. Aissani B, Bernardi G. CpG islands: Features and distribution in the genomes of vertebrates. Gene 1991; 106:173-83.
5. Razin A, Shemer R. DNA methylation in early development. Hum Mol Genet 1995; 4, (Spec No: 1751-5).
6. Okano M, Bell DW, Haber DA, Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 1999; 99:247-57.
7. Chaillet JR, Vogt TF, Beier DR, Leder P. Parental-specific methylation of an imprinted transgene is established during gametogenesis and progressively changes during embryogenesis. Cell 1991; 66:77-83.
8. Reik W, Collick A, Norris ML, Barton SC, Surani MA. Genomic imprinting determines methylation of parental alleles in transgenic mice. Nature 1987; 328:248-51.
9. Howlett SK, Reik W. Methylation levels of maternal and paternal genomes during preimplantation development. Development 1991; 113:119-27.
10. Gruenbaum Y, Cedar H, Razin A. Substrate and sequence specificity of a eukaryotic DNA methylase. Nature 1982; 295:620-2.
11. Leonhardt H, Page AW, Weier HU, Bestor TH. A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei. Cell 1992; 71:865-73.
12. Araujo FD, Knox JD, Szyf M, Price GB, Zannis-Hadjopoulos M. Concurrent replication and methylation at mammalian origins of replication [published erratum appears in Mol Cell Biol 1999 Jun; 19(6):4546]. Mol Cell Biol 1998; 18:3475-82.
13. Weaver IC, et al. Epigenetic programming by maternal behavior. Nat Neurosci 2004; 7:847-54.
14. Weaver IC, et al. Reversal of maternal programming of stress responses in adult offspring through methyl supplementation: Altering epigenetic marking later in life. J Neurosci 2005; 25:11045-54.
15. Fraga MF, et al. Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci USA 2005; 102:10604-9.
16. Jost JP. Nuclear extracts of chicken embryos promote an active demethylation of DNA by excision repair of 5-methyldeoxycytidine. Proc Natl Acad Sci USA 1993; 90:4684-8.
17. Jost JP, Siegmann M, Sun L, Leung R. Mechanisms of DNA demethylation in chicken embryos: Purification and properties of a 5-methylcytosine-DNA glycosylase. J Biol Chem 1995; 270:9734-9.
18. Zhu B, et al. 5-Methylcytosine DNA glycosylase activity is also present in the human MBD4 (G/T mismatch glycosylase) and in a related avian sequence. Nucleic Acids Res 2000; 28:4157-65.
19. Zhu B, et al. 5-methylcytosine-DNA glycosylase activity is present in a cloned G/T mismatch DNA glycosylase associated with the chicken embryo DNA demethylation complex. Proc Natl Acad Sci USA 2000; 97:5135-9.
20. Jost JP, et al. 5-Methylcytosine DNA glycosylase participates in the genome-wide loss of DNA methylation occurring during mouse myoblast differentiation. Nucleic Acids Res 2001; 29:4452-61.
21. Gong Z, et al. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 2002; 111:803-14.
22. Ramchandani S, Bhattacharya SK, Cervoni N, Szyf M. DNA methylation is a reversible biological signal. Proc Natl Acad Sci USA 1999; 96:6107-12, [see comments].
23. Detich N, Bovenzi V, Szyf M. Valproate induces replication-independent active DNA demethylation. J Biol Chem 2003; 278:27586-92.
24. Cervoni N, Szyf M. Demethylase activity is directed by histone acetylation. J Biol Chem 2001; 276:40778-87.
25. Vire E, et al. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 2005.
26. Di Croce L, et al. Methyltransferase recruitment and DNA hypermethylation of target promoters by an oncogenic transcription factor. Science 2002; 295:1079-82.
27. Brenner C, et al. Myc represses transcription through recruitment of DNA methyltransferase corepressor. Embo J 2005; 24:336-46.
28. Meraldi P, Draviam VM, Sorger PK. Timing and checkpoints in the regulation of mitotic progression. Dev Cell 2004; 7:45-60.
29. Chen CY, Olayioye MA, Lindeman GJ, Tang TK. CPAP interacts with 14-3-3 in a cell cycle-dependent manner. Biochem Biophys Res Commun 2006; 342:1203-10.
30. Azzalin CM, Lingner J. The human RNA surveillance factor UPF1 is required for S phase progression and genome stability. Curr Biol 2006; 16:433-9.
31. Goto H, et al. Complex formation of Plk1 and INCENP required for metaphase-anaphase transition. Nat Cell Biol 2006; 8:180-7.
32. 2-phase disrupts microtubule formation and mitotic progression in HeLa cells. Cell Signal 2006; 18:93-104.
33. Marumoto T, et al. Aurora-A kinase maintains the fidelity of early and late mitotic events in HeLa cells. J Biol Chem 2003; 278:51786-95.
34. Fujikawa K, et al. Vav3 is regulated during the cell cycle and effects cell division. Proc Natl Acad Sci USA 2002; 99:4313-8.
35. McManus KJ, Biron VL, Heit R, Underhill DA, Hendzel MJ. Dynamic changes in histone H3 lysine 9 methylations: Identification of a mitosis-specific function for dynamic methylation in chromosome congression and segregation. J Biol Chem 2006; 281:8888-97.
36. Valls E, Sanchez-Molina S, Martinez-Balbas MA. Role of histone modifications in marking and activating genes through mitosis. J Biol Chem 2005; 280:42592-600.
37. Rice JC, et al. Mitotic-specific methylation of histone H4 Lys 20 follows increased PR-Set7 expression and its localization to mitotic chromosomes. Genes Dev 2002; 16:2225-30.
38. Detich N, Ramchandani S, Szyf M. A conserved 3′-untranslated element mediates growth regulation of DNA methyltransferase 1 and inhibits its transforming activity. J Biol Chem 2001; 276:24881-90.
39. Fraga MF, et al. High-performance capillary electrophoretic method for the quantification of 5-methyl 2′-deoxycytidine in genomic DNA: Application to plant, animal and human cancer tissues. Electrophoresis 2002; 23:1677-81.
40. Ramsahoye BH. Nearest-neighbor analysis. Methods Mol Biol 2002; 200:9-15.
41. Yang AS, et al. A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucleic Acids Res 2004; 32:e38.
42. Brueckner B, et al. Epigenetic reactivation of tumor suppressor genes by a novel small-molecule inhibitor of human DNA methyltransferases. Cancer Res 2005; 65:6305-11.
43. Leu YW, et al. Loss of estrogen receptor signaling triggers epigenetic silencing of downstream targets in breast cancer. Cancer Res 2004; 64:8184-92.
44. Nantel A, et al. Transcription profiling of Candida albicans cells undergoing the yeast-to-hyphal transition. Mol Biol Cell 2002; 13:3452-65.
45. Sturn A, Quackenbush J, Trajanoski Z. Genesis: Cluster analysis of microarray data. Bioinformatics 2002; 18:207-8.
46. Clark SJ, Harrison J, Paul CL, Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res 1994; 22:2990-7.
47. Cross SH, Charlton JA, Nan X, Bird AP. Purification of CpG islands using a methylated DNA binding column. Nat Genet 1994; 6:236-44.
48. Heisler LE, et al. CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. Nucleic Acids Res 2005; 33:2952-61.
49. Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol 1987; 196:261-82.
50. Toyota M, Issa JP. Epigenetic changes in solid and hematopoietic tumors. Semin Oncol 2005; 32:521-30.
51. Lee EY, Lee WH. Molecular cloning of the human esterase D gene, a genetic marker of retinoblastoma. Proc Natl Acad Sci USA 1986; 83:6337-41.
52. Greger V, Passarge E, Hopping W, Messmer E, Horsthemke B. Epigenetic changes may contribute to the formation and spontaneous regression of retinoblastoma. Hum Genet 1989; 83:155-8.
53. Takeda S, et al. Identification of surrogate ligands for orphan G protein-coupled receptors. Life Sci 2003; 74:367-77.
54. Kaneko KJ, Rein T, Guo ZS, Latham K, DePamphilis ML. DNA methylation may restrict but does not determine differential gene expression at the Sgy/Tead2 locus during mouse development. Mol Cell Biol 2004; 24:1968-82.
55. Ye W, Zhang L. Heme controls the expression of cell cycle regulators and cell growth in HeLa cells. Biochem Biophys Res Commun 2004; 315:546-54.
56. Masumoto H, Hawke D, Kobayashi R, Verreault A. A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response. Nature 2005; 436:294-8.
57. Boix J, et al. Serum deprivation and protein synthesis inhibition induce two different apoptotic processes in N18 neuroblastoma cells. Exp Cell Res 1998; 238:422-9.
58. Charles I, et al. Serum deprivation induces apoptotic cell death of transformed rat retinal ganglion cells via mitochondrial signaling pathways. Invest Ophthalmol Vis Sci 2005; 46:1330-8.
59. Galli G, Fratelli M. Activation of apoptosis by serum deprivation in a teratocarcinoma cell line: Inhibition by L-acetylcarnitine. Exp Cell Res 1993; 204:54-60.
60. Kulkarni GV, McCulloch CA. Serum deprivation induces apoptotic cell death in a subset of Balb/c 3T3 fibroblasts. J Cell Sci 1994; 107:1169-79.
61. Simm A, Bertsch G, Frank H, Zimmermann U, Hoppe J. Cell death of AKR-2B fibroblasts after serum removal: A process between apoptosis and necrosis. J Cell Sci 1997; 110:819-28.
62. Detich N, Theberge J, Szyf M. Promoter-specific activation and demethylation by MBD2/demethylase. J Biol Chem 2002; 277:35791-4.
63. Bhattacharya SK, Ramchandani S, Cervoni N, Szyf M. A mammalian protein with specific demethylase activity for mCpG DNA. Nature 1999; 397:579-83.
64. Szyf M. Towards a pharmacology of DNA methylation. Trends Pharmacol Sci 2001; 22:350-4.
65. Hoffmann MJ, Schulz WA. Causes and consequences of DNA hypomethylation in human cancer. Biochem Cell Biol 2005; 83:296-321.
66. Qu G, Dubeau L, Narayin A, Yu MC, Ehrlich M. Satellite DNA hypomethylation vs. overall genomic hypomethylation in ovarian epithelial tumors of different malignant potential. Murat Res 1999; 423:91-101.
67. Schuffenhauer S, et al. DNA FISH and complementation studies in ICF syndrome: DNA hypomethylation of repetitive and single copy loci and evidence for a trans acting factor. Hum Genet 1995; 96:562-71.
68. Vairapandi M. Characterization of DNA demethylation in normal and cancerous cell lines and the regulatory role of cell cycle proteins in human DNA demethylase activity. J Cell Biochem 2004; 91:572-83.
69. Szyf M, et al. Cell cycle-dependent regulation of eukaryotic DNA methylase level. J Biol Chem 1985; 260:8653-6.
70. Szyf M, Bozovic V, Tanigawa G. Growth regulation of mouse DNA methyltransferase gene expression. J Biol Chem 1991; 266:10027-30.
71. 1 to S phase transition in normal and tumor cells. Nucleic Acids Res 2000; 28:2108-13.